We propose to further our understanding of the molecular mechanisms that direct stem cells during neural development with the ultimate goal of enabling stem cell based regenerative medicine for neurodegenerative diseases. We will study the etiology of Spinal Muscular Atrophy (SMA) in the context of the mechanisms that we elucidate with the goal of developing clues to potential therapeutic targets for this developmental disease. To understand how external cues direct development, we will elucidate the transcriptional regulatory networks underlying neural development and represent this understanding in predictive computational models. Our studies will begin with undifferentiated embryonic stem (ES) cells, and using protocols that we have pioneered, we will elucidate the mechanism of ES cell development and fate commitment in specific neuron subtypes. Our work is structured into three projects. Project 1 will identify the transcription factors potentially involved in motor neuron identity, iteratively define transcriptional networks, and characterize the transcriptional consequences of SMA. Drawing upon these results, Project 2 will discover how key transcriptional and chromatin regulators control the gene expression programs of mouse and human embryonic stem cells and discover how this regulatory circuitry changes upon differentiation into spinal progenitor cells and then specific classes of central nervous system cells such as motor neurons. Using data from both of these projects, Project 3 will build a model of transcriptional regulation during neural development that integrates expression data, factor binding data, chromatin data, shRNA knock down data, and genome sequence in both human and mouse, examine the gene expression consequences of our SMA model in the context of the deduced regulatory networks, and explore the validity of the mouse model for human ES cell differentiation. Both Project 1 and 2 will test the models produced in Project 3.